ReferenceAndersenThermostat.h

/* Portions copyright (c) 2008-2010 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
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 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
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 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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 */

#ifndef __ReferenceAndersenThermostat_H__
#define __ReferenceAndersenThermostat_H__

#include <vector>

namespace OpenMM {

class ReferenceAndersenThermostat {

   private:
       
   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor
      
         --------------------------------------------------------------------------------------- */

       ReferenceAndersenThermostat();

      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

       ~ReferenceAndersenThermostat();

      /**---------------------------------------------------------------------------------------
      
         Apply the thermostat at the start of a time step.
      
         @param atomGroups         the groups of atoms to apply the thermostat to
         @param atomVelocities     atom velocities
         @param atomMasses         atom masses
         @param temperature        thermostat temperature in Kelvin
         @param collisionFrequency collision frequency for each atom in fs^-1
         @param stepSize           integration step size in fs
                  
         --------------------------------------------------------------------------------------- */
          
      void applyThermostat(const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
              RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const;
      
};

} // namespace OpenMM

#endif // __ReferenceAndersenThermostat_H__